Merge pull request #187 from pepkit/dev_pephub_backend

Add pephub backend to Pipestat

MANIFEST.in

@@ -4,5 +4,6 @@ include pipestat/schemas/*
 include pipestat/backends/*
 include pipestat/backends/file_backend/*
 include pipestat/backends/db_backend/*
+include pipestat/backends/pephub_backend/*
 include pipestat/pipestatreader/*
 include pipestat/jinja_templates/*

pipestat/__init__.py

@@ -3,15 +3,9 @@
 import logmuse
 
 from ._version import __version__
-from .exceptions import PipestatError
 from .const import PKG_NAME
-from .pipestat import (
-    PipestatManager,
-    SamplePipestatManager,
-    ProjectPipestatManager,
-    PipestatBoss,
-)
-
+from .exceptions import PipestatError
+from .pipestat import PipestatBoss, PipestatManager, ProjectPipestatManager, SamplePipestatManager
 
 __all__ = [
     "PipestatError",

pipestat/argparser.py

@@ -2,9 +2,10 @@
 
 import argparse
 import os
+
 from ubiquerg import VersionInHelpParser
-from ._version import __version__
 
+from ._version import __version__
 from .const import ENV_VARS, PKG_NAME, STATUS_SCHEMA
 
 REPORT_CMD = "report"

pipestat/backends/abstract.py

@@ -1,13 +1,13 @@
 import os
 from abc import ABC
 from logging import getLogger
+from typing import Any, Dict, List, Optional, Tuple, Union
+
 from ubiquerg import expandpath
-from typing import List, Dict, Any, Optional, Union, Tuple
 
 from ..const import PKG_NAME, STATUS
-from ..helpers import force_symlink
 from ..exceptions import SchemaError
-
+from ..helpers import force_symlink
 
 _LOGGER = getLogger(PKG_NAME)
 

pipestat/backends/db_backend/db_helpers.py

@@ -2,9 +2,7 @@
 from typing import Any, Dict, List, Optional, Union
 from urllib.parse import quote_plus
 
-
-from sqlmodel import and_, or_, Integer, Float, String, Boolean
-
+from sqlmodel import Boolean, Float, Integer, String, and_, or_
 
 from pipestat.exceptions import MissingConfigDataError
 

pipestat/backends/db_backend/db_parsed_schema.py

@@ -7,11 +7,10 @@
 from typing import Any, Dict, List, Mapping, Optional
 
 from pydantic import ConfigDict, create_model
-
-
 from sqlalchemy import Column, null
 from sqlalchemy.dialects.postgresql import JSONB
 from sqlmodel import Field, SQLModel
+
 from pipestat.const import (
     CANONICAL_TYPES,
     CLASSES_BY_TYPE,
@@ -22,13 +21,13 @@
     PROJECT_NAME,
     RECORD_IDENTIFIER,
     SAMPLE_NAME,
-    STATUS,
     SCHEMA_DESC_KEY,
     SCHEMA_ITEMS_KEY,
     SCHEMA_PROP_KEY,
     SCHEMA_TYPE_KEY,
+    STATUS,
 )
-from pipestat.exceptions import SchemaError, PipestatError
+from pipestat.exceptions import PipestatError, SchemaError
 from pipestat.parsed_schema import ParsedSchema
 
 _LOGGER = logging.getLogger(__name__)

pipestat/backends/db_backend/dbbackend.py

@@ -1,23 +1,24 @@
 import copy
 import datetime
-from logging import getLogger
 from contextlib import contextmanager
-from typing import List, Dict, Any, Optional, Union, NoReturn, Tuple
+from logging import getLogger
+from typing import Any, Dict, List, NoReturn, Optional, Tuple, Union
 
-from sqlmodel import SQLModel, Session, create_engine, select as sql_select
+from sqlmodel import Session, SQLModel, create_engine
+from sqlmodel import select as sql_select
 
-from pipestat.backends.db_backend.db_helpers import selection_filter
 from pipestat.backends.abstract import PipestatBackend
+from pipestat.backends.db_backend.db_helpers import selection_filter
+
+from ...const import CREATED_TIME, MODIFIED_TIME, PKG_NAME, RECORD_IDENTIFIER, STATUS
 from ...exceptions import (
+    ColumnNotFoundError,
     PipestatDatabaseError,
     RecordNotFoundError,
     SchemaError,
-    ColumnNotFoundError,
-    UnrecognizedStatusError,
     SchemaNotFoundError,
+    UnrecognizedStatusError,
 )
-from ...const import PKG_NAME, STATUS, RECORD_IDENTIFIER, CREATED_TIME, MODIFIED_TIME
-
 
 _LOGGER = getLogger(PKG_NAME)
 

pipestat/backends/file_backend/filebackend.py

@@ -1,25 +1,21 @@
 import datetime
-import os.path
 import operator
+import os.path
 from copy import deepcopy
 from functools import reduce
-from itertools import chain
-from ...helpers import get_all_result_files
-
-
 from glob import glob
+from itertools import chain
 from logging import getLogger
-from yacman import FutureYAMLConfigManager as YAMLConfigManager
-from yacman import read_lock, write_lock
+from typing import Any, Callable, Dict, List, Literal, Optional, Tuple, Union
 
 from ubiquerg import create_lock, remove_lock
+from yacman import FutureYAMLConfigManager as YAMLConfigManager
+from yacman import read_lock, write_lock
 
-from typing import List, Dict, Any, Optional, Union, Literal, Callable, Tuple
-
-from ...exceptions import UnrecognizedStatusError, PipestatError
 from ...backends.abstract import PipestatBackend
-from ...const import DATE_FORMAT, PKG_NAME, CREATED_TIME, MODIFIED_TIME, META_KEY, HISTORY_KEY
-
+from ...const import CREATED_TIME, DATE_FORMAT, HISTORY_KEY, META_KEY, MODIFIED_TIME, PKG_NAME
+from ...exceptions import PipestatError, UnrecognizedStatusError
+from ...helpers import get_all_result_files
 
 _LOGGER = getLogger(PKG_NAME)
 
@@ -46,7 +42,7 @@ def __init__(
             this object method calls
         :param str pipeline_name: name of pipeline associated with result
         :param str pipeline_type: "sample" or "project"
-        :param str parsed_schema: results output schema. Used to construct DB columns.
+        :param str parsed_schema: results output schema.
         :param str status_schema: schema containing pipeline statuses e.g. 'running'
         :param str status_file_dir: directory for placing status flags
         :param str result_formatter: function for formatting result